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Crystal structure of human SP100 in complex with bromodomain-focused fragment FM009493b 2,3-Dimethoxy-2,3-dimethyl-2,3-dihydro-1,4-benzodioxin-6-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 277 17-23% PEG20K, 0.1M MES 6.1, 2-4% Ethylene glycol, 4 days
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.855 α = 90 b = 45.429 β = 101.77 c = 83.715 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2014-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.35 28.59 97.8 0.03 0.041 0.028 0.998 16 3.3 101393
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.38 93.3 0.547 0.74 0.495 0.615 1.5 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Internal 1.35 28.589 1.34 101332 5097 97.55 0.1392 0.1375 0.1389 0.1738 0.1749
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.455 f_angle_d 1.402 f_chiral_restr 0.228 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2881 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing